This application responds to the NHGRI's Medical Sequencing Discovery Projects emphasis. Primary open angle glaucoma (POAG) is the most frequent form of glaucoma in the United States and a leading cause of irreversible blindness and visual impairment worldwide. POAG affects more than 2.25 million Americans over age 40. Each year, it causes blindness in ~100,000 Americans and 3 million people worldwide. Treatments for POAG slow progression of the disease but do not reverse glaucomatous damage. Thus, early detection is key in effective management of glaucoma and prevention of further damage. Genetic variation has been shown to have a critical role in the occurrence and development of POAG. The disease has heritability, where first-degree relatives of subjects with POAG have been found to have a risk to develop disease 7-10 times greater than that of the general population, and a high concordance has been observed between monozygotic twins. A number of studies have performed genome-wide scans for glaucoma susceptibility loci and have yielded several loci with POAG association. The number of loci identified provides strong evidence for a polygenic nature of POAG. We propose to study POAG using a novel dual approach: genome-wide targeted gene sequencing complemented by a study of copy number variation in 350 POAG cases and 350 controls. We will leverage two large projects aimed to genotype a large number of POAG cases and controls. The NHGRI-funded GENEVA GLAUGEN consortium is genotyping ~660,000 loci for 2400 samples including 450 POAG cases and 400 controls collected at Massachusetts Eye and Ear Infirmary, and the NEIGHBOR consortium is expected to do the same for ~4000 samples including samples from 600 POAG cases and 600 controls collected at UCSD. While these consortia will discover common loci that increase the risk of POAG, we will take a complementary approach and identify rare variants that may cause POAG. Together, these consortia provide a unique opportunity to blend knowledge gleaned from SNP array data with genome-wide targeted gene sequencing and genome structure data. We will use a novel but proven sequencing strategy to identify coding variants in which all exons with some flanking intron are sequenced, approximately 30 million bases per patient, at 25- times coverage. We will identify point mutations, small insertions and deletions and structural variations, analyze them statistically under the Common Disease Rare Variants (CD-RV) hypothesis, and confirm identified genes and variants in additional patients. The work proposed here uses sequencing technology and computational analysis of sequence data to advance knowledge and understanding of genetic causes of glaucoma, and improve the lifestyle through early diagnosis of the millions that are at risk of being afflicted. PUBLIC HEALTH RELEVANCE: Primary open angle glaucoma (POAG) is the most common form of glaucoma in the United States and a leading cause of irreversible blindness and visual impairment worldwide, affecting more than 2 million Americans over age 40, and causing blindness in ~100,000 Americans and 3 million people worldwide each year. Treatments for the disease can slow progression but do not reverse damage, so early detection is the key for effective disease management and prevention of further damage;so to find genomic variations associated with POAG, a disease with high heritability and with no remedial treatment, this research will use a novel dual approach to genome-wide association study: re-sequence all exons from protein-coding genes in 350 cases and 350 controls, and simultaneously, study copy number variation to find disease-associated single point mutations, small insertions and deletions, and genome structure variations. This research could have considerable public health benefit by identifying genes and their variants associated with pathogenesis of the disease, leading to new strategies for early diagnosis and treatment, inhibition of vision loss, and possibly provide an avenue to prevention.